**fishR » R**, and kindly contributed to R-bloggers)

I mentioned previously, that I have been updating the Mark-Recapture vignettes. That has morphed into a document that is an update of the Mark-Recapture Closed and Open vignettes and the depletion/removal vignettes and associated FSA functions. Some of the changes are cosmetic, others are more important. I attempt to highlight the changes below but you should also see the NEWS file for the FSA package. The new vignette is here.

## FSA changes

`capHistConvert()`

— major changes, should consider this to be a new function.`capHistSum()`

— added an`m.array`

object to the output, changed column and row labels to the methodB objects, and added a`plot()`

object to make the diagnostic plots identified in the Rcapture package. Old code should still work.`depletion()`

— Changed`type=`

to`method=`

and added`DeLury`

as an option to`method=`

(and left`Delury`

). Changed`ricker.mod=`

to`Ricker.mod=`

. Old code that explicitly used`type=`

will be broken (need to change to`method=`

).`mrClosed()`

— Changed`incl.inputs=`

to`verbose=,`

changed`type=`

to`method=`

. Added the ability to construct a CI for the overall PE when multiple groups are used in a Petersen family method (thus, added a`incl.all=`

to`confint()`

). Changed default for`incl.all=`

from`FALSE`

to`TRUE`

. Old code that explicitly used`type=`

will be broken (need to change to`method=`

).`mrOpen()`

— Changed`ci.type=`

to`type=`

and`phi.type=`

to`phi.full=`

. Removed`type=`

from`summary()`

and added a`verbose=`

which will print only the estimates if`FALSE`

or both observables and estimates if`TRUE`

. Added a`verbose=`

to`confint()`

to control whether the message about the type of confidence interval is printed or not. Added another function,`jolly()`

, that is the same as`mrOpen()`

. Old code should work unless`ci.type=`

and`phi.type=`

were used in`mrOpen()`

or`type=`

was used in`summary()`

.`removal()`

— Added options to perform Moran (1951) and Schnute (1983) removal methods. Completely modified the code so that the examples with`apply()`

and`lapply()`

would also provide confidence intervals. Changed so that if catch is a one row or one column matrix or data.frame then it will be converted to a vector, which allows one to extract one row from a data.frame to send to`removal()`

without having to use`as.numeric()`

. Old code should still work.

## New Abundance Vignette

Again, this is now a combination of the original M-R closed, M-R open, and depletion/removal events. All sections are like the original except for the changes in FSA from above and the theoretical development is greatly reduced.

The M-R closed section now includes an illustration to estimate N using the Petersen methods if the data is grouped (i.e., separate estimates by length groups) and for fitting the Otis et al. (1978) log-linear models to multiple M-R data with possible capture probability heterogeneities (using the Rcapture package).

The M-R open section now includes a section on fitting log-linear models (using Rcapture package).

The depletion/removal now includes is a section on using the method of Schnute (1983) to identify a statistically different capture probability for the first sample.

Filed under: Administration, Fisheries Science, R Tagged: Abundance, Depletion, FSA, Jolly-Seber, Mark-Recapture, R, Removal

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